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You have just rephrased "it worked, now it's broken"
There's no new information that helps anyone help you.
Post a link to the " recommended way" that you are using, so that others can see exactly what that is
Are you using heirarchies, or just simple tags?
Then run some tests:
E.g. if you open a book which suddenly has a wrong genre, is that genre shown in book details and on the edit metadata screen.? If you fix it in edit metadata , does it stay fixed. If you create a new test genre and assign it to exactly one book, does it stay like that?
Screenshots often help.
Is your calibre folder on a networked drive or being synced to a cloud such as one drive?
What version of calibre and did the problem start after some calibre or windows update?
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